The configuration file you recently created will serve as the new stylesheet for your DocBook document. So basically everything you have to do is to instruct your XSLT processor to convert your document using the stylesheet. I assume you don't to this for the first time, but nevertheless provide an example here using xsltproc:
xsltproc /usr/local/etc/annotate.conf
/your/document.xml Please make sure that the
HTML files which your XSLT processor outputs are put into the directory
that you specified in the configuration. This is the value of the
DocumentRoot variable.Important